BMRB Entry 15860

Name: NMR solution structure of modified DNA containing imidazole nucleosides at acidic, neutral and basic pH
Published: 2009-10-12

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PDB ID: 2k67
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15860
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of modified DNA containing imidazole nucleosides at acidic, neutral and basic pH

Deposition date:

2008-07-04

Original release date:

2009-10-12

Authors:

Johannsen, Silke; Boehme, Dominik; Duepre, Nicole; Mueller, Jens; Sigel, Roland

Citation:

Citation: Johannsen, Silke; Boehme, Dominik; Duepre, Nicole; Mueller, Jens; Sigel, Roland. "Solution structure at different pHs of a DNA hairpin containing artificial nucleotides" .

Assembly members:

Assembly members:
DNA_17-mer, polymer, 17 residues, 5021.597 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_17-mer: TTAATTTXXXAAATTAA

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	502

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_17-mer	1

Entities:

Entity 1, DNA_17-mer 17 residues - 5021.597 Da.

1

DT

DA

DT

D33

2

DA

DT

DA

Samples:

sample_1: DNA 17-mer 0.2-0.8 mM; sodium perchlorate 120 mM

sample_2: DNA 17-mer 0.2-0.8 mM; sodium perchlorate 120 mM

sample_conditions_1: ionic strength: 0.12 M; pD: 4.7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 4.7; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 0.12 M; pD: 7.2; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 120 mM; pH: 7.2; pressure: 1 atm; temperature: 278 K

sample_conditions_5: ionic strength: 0.12 M; pD: 10.2; pressure: 1 atm; temperature: 298 K

sample_conditions_6: ionic strength: 120 mM; pH: 10.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_5
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_5
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_5
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_6

Software:

TOPSPIN v1.3, 2.0, 2.1, Bruker Biospin - processing

SPARKY v3.1, Goddard - chemical shift assignment, data analysis, peak picking

DYANA v1.5, Guntert, Braun and Wuthrich - structure solution

X-PLOR NIH v2.15, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 700 MHz